Conservation of Nucleosome Positions in Duplicated and Orthologous Gene Pairs

Although nucleosome positions tend to be conserved in gene promoters, whether they are conserved in duplicated and orthologous genes is unknown. In order to elucidate how nucleosome positions are conserved between duplicated and orthologous gene pairs, I performed 2 comparative studies. First, I compared the nucleosome position profiles of duplicated genes in the filamentous ascomycete Aspergillus fumigatus. After identifying 63 duplicated gene pairs among 9630 protein-encoding genes, I compared the nucleosome position profiles of the paired genes. Although nucleosome positions are conserved more in gene promoters than in gene bodies, their profiles were diverse, suggesting evolutionary changes after gene duplication. Next, I examined the conservation of nucleosome position profiles in 347 A. fumigatus orthologs of S. cerevisiae genes that showed notably high conservation of nucleosome positions between the parent strain and 2 deletion mutants. In only 11 (3.2%) of the 347 gene pairs, the nucleosome position profile was highly conserved (Spearman's rank correlation coefficient > 0.7). The absence of nucleosome position conservation in promoters of orthologous genes suggests organismal specificity of nucleosome arrangements.


Introduction
Nucleosomes are histone octamers around which DNA is wrapped in 1.65 turns [1]. Neighboring nucleosomes are separated by unwrapped linker DNA. Nucleosome density is lower, and nucleosome position is more conserved in the promoters than in the bodies of genes [2][3][4][5]. It is thought that nucleosome positioning in the gene promoter plays an important role in transcriptional regulation.
Although nucleosome positions can be partially simulated using a DNA-sequence-based approach [6], these simulations are limited due to variations between species. The nucleosome positioning mechanism varies between the 2 ascomycetous yeasts, Saccharomyces cerevisiae, and Schizosaccharomyces pombe [7]. Nucleosome positioning differs even among phylogenetically close ascomycetous yeast species [5].
Gene duplication is a driving force behind gene creation, and generating novel functions in newly created genes. Approximately one-half of cellular functions have been gained through gene duplication [8]. The duplicated genes encode similar amino acid sequences and often similar protein functions. It is uncertain, however, whether duplicated genes have similar nucleosome position profiles. In this study, I compared nucleosome positions in the promoter and body regions of duplicated gene pairs in the filamentous ascomycete Aspergillus fumigatus.
Previous analyses have found that nucleosome positions in A. fumigatus are conserved more in gene promoters than in gene bodies, even after treatment with the histone deacetylase inhibitor trichostatin A [4,9]. In addition, nucleosome positions in S. cerevisiae are more conserved in gene promoters than in gene bodies between the control and the histone acetyltransferase gene ELP3 deletion mutant, and between the control and the histone deacetylase gene HOS2 deletion mutant [10]. The proteins Elp3 and Hos2 show the highest and the third highest evolutionary conservation, respectively, among the fungal histone modification proteins [11].
How well are nucleosome positions conserved in genes of the same origins? If there is a "nucleosome position code" that regulates nucleosome positioning, common nucleosome 2 The Scientific World Journal Promoter Body of nucleosome positioning between A. fumigatus and S. cerevisiae, I focused on 466 genes ( Table 3) that showed notably high conservation of nucleosome positioning in the promoters of the control and the ELP3 and HOS2 deletion mutants from the previous study [10]. A total of 3339 ortholog clusters were identified (See table 1 in Supplementary Material available at doi: 10.1100/2012/298174) between A. fumigatus and S. cerevisiae by ortholog cluster analysis in the Microbial Genome Database for Comparative Analysis (MBGD, http://mbgd .nibb.ac.jp/) [12]. Of these orthologous gene pairs, 347 (Table 4) are yeast genes that showed a high level of nucleosome positioning conservation in the control and deletion mutants. I focused on these 347 orthologous pairs to compare nucleosome positioning between species. The same number of pairs of A. fumigatus and S. cerevisiae genes chosen at random were used as a control.

Nucleosome Position Profile.
Nucleosome mapping numbers at each genomic position were determined [13] based The Scientific World Journal 7          on genome-wide nucleosome mapping data for A. fumigatus [9] and S. cerevisiae [10]. In this analysis, a 1-kb region upstream of the translational start site was defined as a gene promoter. When the length of the gene body region is more than 1 kb, a 1-kb region downstream of the translational start site was defined as the gene body. When the length of the gene body is less than 1 kb, the region between the translational start and end sites was defined as the gene body. Analyses of nucleosome position data including calculation of Spearman's rank correlation coefficient were performed using the statistics software R (http://www.r-project.org/).

Nucleosome Position Profiles of Duplicated Genes in
Aspergillus fumigatus. I compared nucleosome position profiles in each of the 63 duplicated gene pairs. Nucleosome positioning was conserved more in gene promoters than in gene bodies (Figure 1), as observed in the comparison of nucleosome positioning between trichostatin A-treated and -untreated A. fumigatus [4]. This result suggests that nucleosome positioning in the gene promoter plays an important role in transcriptional regulation [14].     Single-gene duplications and gene cluster duplications consisting of multiple genes were identified. One cluster of 4 genes (AFUA 1G00420 to AFUA 1G00470) is a duplication of another 4-gene cluster (AFUA 8G04120 to AFUA 8G04080) ( Table 2). Among these gene pairs, the nucleosome position profile was poorly conserved in the gene promoter between AFUA 1G00470 and AFUA 8G04080 and in the gene body between AFUA 1G00440 and AFUA 8G04110 (Spearman's rank correlation coefficients were 0.43 and 0.23, resp.) ( Table 2). With the exception of these 2 cases, the nucleosome position profile was highly conserved (correlation coefficients were higher than 0.7) ( Table 2).